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Cancer Research UK Cambridge Institute

 

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Proteomics core facility

The Proteomics core facility focuses on the systematic study of proteins, particularly their structures, interactions and expression levels.  The facility is equipped with state-of-the-art instrumentation for CRUK CI researchers requiring access to proteomics technology and expertise.

The Proteomics core facility provides help in designing experimental strategies and implements and validates previously developed proteomic workflows to profile proteins from diverse biological samples. We also aim to modify or develop entirely new methods and assays when warranted. In addition, we have bioinformatics support for data management and analysis. 

The facility has already been well equipped with state-of-the-art analytical instrumentation for proteomic studies, including the latest Orbitrap mass spectrometers: a LTQ Velos Orbitrap (Thermo), and a newly acquired (2013) Q Exactive Orbitrap both are configured to a Dionex Ultimate 3000 RSLC nanoHPLC system. The mass spectrometers are supported by off-line chromatography platforms: two Dionex Ultimate 3000 capHPLC systems for multidimensional chromatography at the protein and peptide level. 1D and 2D gel electrophoresis systems are available in the equipment park run by Jane Gray. Data analysis is supported by an array of bioinformatics and statistical analysis tools.

Specific methods and areas of interest include:

Protein profiling of complex biological samples, e.g. tissue, cell extracts

  • Profiling by nanoLC/MS
  • Multidimensional protein/peptide fractionation by capLC and/or geLC

Targeted protein identification by nanoLC/MS/MS

  • Coomassie and silver stained gel bands of purified proteins
  • In solution digestion of purified proteins
  • Multiple reaction monitoring of defined peptides

Identification of protein and peptide modifications

  • Phosphorylation sites

Relative quantitation by nanoLC/MS/MS

  • SILAC - stable isotope labeling of amino acids in cell culture
  • ITRAQ - an isobaric peptide tagging system
  • MRM: multiple reaction monitoring